KIRC - KIRP - KICH analysis on AXL, MET and SRC
library(TCGAplot)## Warning: package 'TCGAplot' was built under R version 4.2.2## Loading required package: ggpubr## Loading required package: ggplot2## ## Registered S3 methods overwritten by 'treeio':
## method from
## MRCA.phylo tidytree
## MRCA.treedata tidytree
## Nnode.treedata tidytree
## Ntip.treedata tidytree
## ancestor.phylo tidytree
## ancestor.treedata tidytree
## child.phylo tidytree
## child.treedata tidytree
## full_join.phylo tidytree
## full_join.treedata tidytree
## groupClade.phylo tidytree
## groupClade.treedata tidytree
## groupOTU.phylo tidytree
## groupOTU.treedata tidytree
## is.rooted.treedata tidytree
## nodeid.phylo tidytree
## nodeid.treedata tidytree
## nodelab.phylo tidytree
## nodelab.treedata tidytree
## offspring.phylo tidytree
## offspring.treedata tidytree
## parent.phylo tidytree
## parent.treedata tidytree
## root.treedata tidytree
## rootnode.phylo tidytree
## sibling.phylo tidytree## Warning: replacing previous import 'enrichplot::color_palette' by
## 'ggpubr::color_palette' when loading 'TCGAplot'## ## Warning: replacing previous import 'ComplexHeatmap::pheatmap' by
## 'pheatmap::pheatmap' when loading 'TCGAplot'## Registered S3 methods overwritten by 'fmsb':
## method from
## print.roc pROC
## plot.roc pROC## TCGAplot v7.0.0
##
## If you use TCGAplot in published research, please cite:
## Liao C, Wang X. TCGAplot: an R package for integrative pan-cancer analysis and visualization of TCGA multi-omics data. BMC Bioinformatics. 2023 Dec 17;24(1):483.AXL, MET and SRC expression across PanCancer
gene1 <- 'AXL'
gene2 <- 'MET'
gene3 <- 'SRC'
pan_boxplot(gene1,palette="jco",legend="right",method="wilcox.test")
pan_boxplot(gene2,palette="jco",legend="right",method="wilcox.test")
pan_boxplot(gene3,palette="jco",legend="right",method="wilcox.test")
## paired boxplot
pan_paired_boxplot(gene1,palette="jco",legend="right",method="wilcox.test")
pan_paired_boxplot(gene2,palette="jco",legend="right",method="wilcox.test")
pan_paired_boxplot(gene3,palette="jco",legend="right",method="wilcox.test")
gene1 <- 'AXL'
gene2 <- 'MET'
gene3 <- 'SRC'
# AXL
axl_kirc_exp <- paired_boxplot('KIRC',gene1, palette="aaas",legend="none",label="p.signif",method="wilcox.test")
axl_kirp_exp <- paired_boxplot('KIRP',gene1, palette="aaas",legend="none",label="p.signif",method="wilcox.test")
axl_kich_exp <- paired_boxplot('KICH',gene1, palette="aaas",legend="none",label="p.signif",method="wilcox.test")
# MET
met_kirc_exp <- paired_boxplot('KIRC',gene2, palette="aaas",legend="none",label="p.signif",method="wilcox.test")
met_kirp_exp <- paired_boxplot('KIRP',gene2, palette="aaas",legend="none",label="p.signif",method="wilcox.test")
met_kich_exp <- paired_boxplot('KICH',gene2, palette="aaas",legend="none",label="p.signif",method="wilcox.test")
# SRC
src_kirc_exp <- paired_boxplot('KIRC',gene3, palette="aaas",legend="none",label="p.signif",method="wilcox.test")
src_kirp_exp <- paired_boxplot('KIRP',gene3, palette="aaas",legend="none",label="p.signif",method="wilcox.test")
src_kich_exp <- paired_boxplot('KICH',gene3, palette="aaas",legend="none",label="p.signif",method="wilcox.test")
# save Files - AXL
png("/Users/tulaykarakulak/Desktop/AXLPaper/Figures/TCGAPlot/axl_kirc_exp.png", width = 8 * 300, height = 8 * 300, res = 300, bg = "transparent")
print(axl_kirc_exp)
dev.off()## quartz_off_screen
## 2png("/Users/tulaykarakulak/Desktop/AXLPaper/Figures/TCGAPlot/axl_kirp_exp.png", width = 8 * 300, height = 8 * 300, res = 300, bg = "transparent")
print(axl_kirp_exp)
dev.off()## quartz_off_screen
## 2png("/Users/tulaykarakulak/Desktop/AXLPaper/Figures/TCGAPlot/axl_kich_exp.png", width = 8 * 300, height = 8 * 300, res = 300, bg = "transparent")
print(axl_kich_exp)
dev.off()## quartz_off_screen
## 2# save Files - MET
png("/Users/tulaykarakulak/Desktop/AXLPaper/Figures/TCGAPlot/met_kirc_exp.png", width = 8 * 300, height = 8 * 300, res = 300, bg = "transparent")
print(met_kirc_exp)
dev.off()## quartz_off_screen
## 2png("/Users/tulaykarakulak/Desktop/AXLPaper/Figures/TCGAPlot/met_kirp_exp.png", width = 8 * 300, height = 8 * 300, res = 300, bg = "transparent")
print(met_kirp_exp)
dev.off()## quartz_off_screen
## 2png("/Users/tulaykarakulak/Desktop/AXLPaper/Figures/TCGAPlot/met_kich_exp.png", width = 8 * 300, height = 8 * 300, res = 300, bg = "transparent")
print(met_kich_exp)
dev.off()## quartz_off_screen
## 2# save Files - SRC
png("/Users/tulaykarakulak/Desktop/AXLPaper/Figures/TCGAPlot/src_kirc_exp.png", width = 8 * 300, height = 8 * 300, res = 300, bg = "transparent")
print(src_kirc_exp)
dev.off()## quartz_off_screen
## 2png("/Users/tulaykarakulak/Desktop/AXLPaper/Figures/TCGAPlot/src_kirp_exp.png", width = 8 * 300, height = 8 * 300, res = 300, bg = "transparent")
print(src_kirp_exp)
dev.off()## quartz_off_screen
## 2png("/Users/tulaykarakulak/Desktop/AXLPaper/Figures/TCGAPlot/src_kich_exp.png", width = 8 * 300, height = 8 * 300, res = 300, bg = "transparent")
print(src_kich_exp)
dev.off()## quartz_off_screen
## 2tumor mutational burden of a gene across cancers
gene_TMB_radar(gene1)
gene_TMB_radar(gene2)
gene_TMB_radar(gene3)
ggsave('/Users/tulaykarakulak/Desktop/AXLPaper/Figures/TCGAPlot/axl_tmb.png', plot = gene_TMB_radar(gene1), bg = "transparent", width = 7, height = 7)
ggsave('/Users/tulaykarakulak/Desktop/AXLPaper/Figures/TCGAPlot/met_tmb.png', plot = gene_TMB_radar(gene2), bg = "transparent", width = 7, height = 7)
ggsave('/Users/tulaykarakulak/Desktop/AXLPaper/Figures/TCGAPlot/src_tmb.png', plot = gene_TMB_radar(gene3), bg = "transparent", width = 7, height = 7)cancer1 <- 'KIRC'
cancer2 <- 'KIRP'
cancer3 <- 'KICH'
gene_stage(cancer1,gene1,add = "jitter",palette="jco",legend="none",label="p.signif",method="wilcox.test")
gene_stage(cancer1,gene2,add = "jitter",palette="jco",legend="none",label="p.signif",method="wilcox.test")
gene_stage(cancer1,gene3,add = "jitter",palette="jco",legend="none",label="p.signif",method="wilcox.test")
gene_stage(cancer2,gene1,add = "jitter",palette="jco",legend="none",label="p.signif",method="wilcox.test")## Warning in wilcox.test.default(c(6.41, 5.88, 6.11, 6.29, 5.73, 5.47, 5.12, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(6.41, 5.88, 6.11, 6.29, 5.73, 5.47, 5.12, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(5.1, 4.73, 5.18, 4.8, 5.15, 5.3, 4.11, :
## cannot compute exact p-value with ties
gene_stage(cancer2,gene2,add = "jitter",palette="jco",legend="none",label="p.signif",method="wilcox.test")## Warning in wilcox.test.default(c(8.27, 7.78, 7.77, 6.64, 7.02, 8.09, 9.24, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(8.27, 7.78, 7.77, 6.64, 7.02, 8.09, 9.24, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(7.45, 6.73, 6.32, 6.96, 7.97, 5.79, 7.3, :
## cannot compute exact p-value with ties
gene_stage(cancer2,gene3,add = "jitter",palette="jco",legend="none",label="p.signif",method="wilcox.test")## Warning in wilcox.test.default(c(6.28, 4.78, 5.24, 5.81, 5.23, 6.26, 7.62, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(6.28, 4.78, 5.24, 5.81, 5.23, 6.26, 7.62, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(4.88, 5.9, 5.05, 4.73, 6.43, 5.08, 5.34, :
## cannot compute exact p-value with ties
gene_stage(cancer3,gene1,add = "jitter",palette="jco",legend="none",label="p.signif",method="wilcox.test")## Warning in wilcox.test.default(c(3.49, 1.57, 1.41, 3.29, 3.31, 2.04, 1.23, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(3.49, 1.57, 1.41, 3.29, 3.31, 2.04, 1.23, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(3.49, 1.57, 1.41, 3.29, 3.31, 2.04, 1.23, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(2.44, 3.17, 2.82, 1.51, 2.75, 3.4, 1.14, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(2.07, 2.81, 2.24, 2.37, 2.01, 2.46, 2.67, :
## cannot compute exact p-value with ties
gene_stage(cancer3,gene2,add = "jitter",palette="jco",legend="none",label="p.signif",method="wilcox.test")## Warning in wilcox.test.default(c(6.19, 5.16, 5.48, 8.9, 4.44, 8.04, 4.64, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(6.19, 5.16, 5.48, 8.9, 4.44, 8.04, 4.64, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(6.19, 5.16, 5.48, 8.9, 4.44, 8.04, 4.64, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(8.53, 5.69, 7.66, 6.89, 7.32, 7.66, 6.13, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(8.53, 5.69, 7.66, 6.89, 7.32, 7.66, 6.13, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(7.13, 8.42, 6.43, 5.39, 6.41, 6.44, 5.28, :
## cannot compute exact p-value with ties
gene_stage(cancer3,gene3,add = "jitter",palette="jco",legend="none",label="p.signif",method="wilcox.test")## Warning in wilcox.test.default(c(3.6, 3.2, 2.23, 5.38, 4.54, 3.59, 2.44, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(3.6, 3.2, 2.23, 5.38, 4.54, 3.59, 2.44, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(5.53, 4, 3.56, 3.59, 4.45, 5.73, 3.07, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(5.53, 4, 3.56, 3.59, 4.45, 5.73, 3.07, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(4.01, 4.45, 3.69, 3.69, 4.57, 3.97, 3.33, :
## cannot compute exact p-value with ties
ggsave('/Users/tulaykarakulak/Desktop/AXLPaper/Figures/TCGAPlot/src_stage.png', plot = gene_stage(cancer1,gene3,add = "jitter",palette="jco",legend="none",label="p.signif",method="wilcox.test"), bg = "transparent", width = 7, height = 7)gene_deg_heatmap(cancer1, gene1,top_n=20)
maybe not so important ## Age
gene_3age("KIRC","AXL", age1=40, age2=60)
gene_3age("KIRC","MET", age1=40, age2=60)
gene_3age("KIRC","SRC", age1=40, age2=60)
gene_3age("KIRP","AXL", age1=40, age2=60)
gene_3age("KIRP","MET", age1=40, age2=60)
gene_3age("KIRP","SRC", age1=40, age2=60)
gene_3age("KICH","AXL", age1=40, age2=60)## Warning in wilcox.test.default(c(1.57, 1.51, 2.75, 2.81, 3.4, 3.31, 2.04, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(2.44, 3.49, 2.04, 3.26, 3.17, 1.41, 3.29, :
## cannot compute exact p-value with ties
gene_3age("KICH","MET", age1=40, age2=60)## Warning in wilcox.test.default(c(5.16, 6.89, 7.32, 8.42, 7.66, 4.44, 8.04, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(5.16, 6.89, 7.32, 8.42, 7.66, 4.44, 8.04, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(8.53, 6.19, 7.43, 7.04, 5.69, 5.48, 8.9, :
## cannot compute exact p-value with ties
gene_3age("KICH","SRC", age1=40, age2=60)## Warning in wilcox.test.default(c(3.2, 3.59, 4.45, 4.45, 5.73, 4.54, 3.59, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(3.2, 3.59, 4.45, 4.45, 5.73, 4.54, 3.59, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(5.53, 3.6, 3.68, 3.8, 4, 2.23, 5.38, 3.07, :
## cannot compute exact p-value with ties
gene_gene_scatter(cancer1,gene1,gene2,density="F")
gene_gene_scatter(cancer1,gene1,gene3,density="F")
gene_gene_scatter(cancer1,gene2,gene3,density="F")
gene_gene_scatter(cancer2,gene1,gene2,density="F")
gene_gene_scatter(cancer2,gene1,gene3,density="F")
gene_gene_scatter(cancer2,gene2,gene3,density="F")
gene_gene_scatter(cancer3,gene1,gene2,density="F")
gene_gene_scatter(cancer3,gene1,gene3,density="F")
gene_gene_scatter(cancer3,gene2,gene3,density="F")
tcga_roc(cancer1,gene1)## Setting direction: controls < cases## Warning in geom_segment(aes(x = 0, xend = 1, y = 0, yend = 1), color = "darkgrey", : All aesthetics have length 1, but the data has 514 rows.
## ℹ Did you mean to use `annotate()`?
tcga_roc(cancer1,gene2)## Setting direction: controls < cases## Warning in geom_segment(aes(x = 0, xend = 1, y = 0, yend = 1), color = "darkgrey", : All aesthetics have length 1, but the data has 514 rows.
## ℹ Did you mean to use `annotate()`?
tcga_roc(cancer1,gene3)## Setting direction: controls < cases## Warning in geom_segment(aes(x = 0, xend = 1, y = 0, yend = 1), color = "darkgrey", : All aesthetics have length 1, but the data has 514 rows.
## ℹ Did you mean to use `annotate()`?
tcga_roc(cancer2,gene1)## Setting direction: controls < cases## Warning in geom_segment(aes(x = 0, xend = 1, y = 0, yend = 1), color = "darkgrey", : All aesthetics have length 1, but the data has 514 rows.
## ℹ Did you mean to use `annotate()`?
tcga_roc(cancer2,gene2)## Setting direction: controls < cases## Warning in geom_segment(aes(x = 0, xend = 1, y = 0, yend = 1), color = "darkgrey", : All aesthetics have length 1, but the data has 514 rows.
## ℹ Did you mean to use `annotate()`?
tcga_roc(cancer2,gene3)## Setting direction: controls < cases## Warning in geom_segment(aes(x = 0, xend = 1, y = 0, yend = 1), color = "darkgrey", : All aesthetics have length 1, but the data has 514 rows.
## ℹ Did you mean to use `annotate()`?
tcga_roc(cancer3,gene1)## Setting direction: controls > cases## Warning in geom_segment(aes(x = 0, xend = 1, y = 0, yend = 1), color = "darkgrey", : All aesthetics have length 1, but the data has 514 rows.
## ℹ Did you mean to use `annotate()`?
tcga_roc(cancer3,gene2)## Setting direction: controls < cases## Warning in geom_segment(aes(x = 0, xend = 1, y = 0, yend = 1), color = "darkgrey", : All aesthetics have length 1, but the data has 514 rows.
## ℹ Did you mean to use `annotate()`?
tcga_roc(cancer3,gene3)## Setting direction: controls > cases## Warning in geom_segment(aes(x = 0, xend = 1, y = 0, yend = 1), color = "darkgrey", : All aesthetics have length 1, but the data has 514 rows.
## ℹ Did you mean to use `annotate()`?
Survival Analysis
tcga_kmplot(cancer1,gene1,palette='jco')
tcga_kmplot(cancer1,gene2,palette='jco')
tcga_kmplot(cancer1,gene3,palette='jco')
tcga_kmplot(cancer2,gene1,palette='jco')
tcga_kmplot(cancer2,gene2,palette='jco')
tcga_kmplot(cancer2,gene3,palette='jco')
tcga_kmplot(cancer3,gene1,palette='jco')
tcga_kmplot(cancer3,gene2,palette='jco')
tcga_kmplot(cancer3,gene3,palette='jco')
Mutation Data of AXL, MET and SRC
# KIRC
library(TCGAbiolinks)
query_kirc <- GDCquery(
project = c("TCGA-KIRC"),
data.category = "Simple Nucleotide Variation",
access = "open",
data.type = "Masked Somatic Mutation",
workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking"
)## --------------------------------------## o GDCquery: Searching in GDC database## --------------------------------------## Genome of reference: hg38## --------------------------------------------## oo Accessing GDC. This might take a while...## --------------------------------------------## ooo Project: TCGA-KIRC## --------------------## oo Filtering results## --------------------## ooo By access## ooo By data.type## ooo By workflow.type## ----------------## oo Checking data## ----------------## ooo Checking if there are duplicated cases## ooo Checking if there are results for the query## -------------------## o Preparing output## -------------------GDCdownload(query_kirc)## Downloading data for project TCGA-KIRC## Of the 412 files for download 412 already exist.## All samples have been already downloadedmaf_kirc <- GDCprepare(query_kirc)## indexed 373.00B in 0s, 33.29MB/s indexed 1.00TB in 0s, 2.79PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.22PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.83PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.57PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.11PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.70PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.95PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.47PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.15PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.11PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.07PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.91PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 2.64PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.96PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.02PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.25PB/s indexed 373.00B in 0s, 52.15MB/s indexed 1.00TB in 0s, 2.51PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.54PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 2.29PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.60PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.16PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.61PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.93PB/s indexed 373.00B in 0s, 92.03MB/s indexed 1.00TB in 0s, 1.99PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.28PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.61PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.92PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.02PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.95PB/s indexed 373.00B in 0s, 53.95MB/s indexed 1.00TB in 0s, 1.28PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.42PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.77PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.08PB/s indexed 373.00B in 0s, 74.50MB/sindexed 1.00TB in 0s, 896.03TB/s indexed 373.00B in 0s, 62.58MB/sindexed 1.00TB in 0s, 909.24TB/s indexed 373.00B in 0s, 92.03MB/s indexed 1.00TB in 0s, 2.33PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 3.73PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.46PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.38PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.93PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.27PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.88PB/s indexed 373.00B in 0s, 53.95MB/s indexed 1.00TB in 0s, 2.61PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.67PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.96PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.30PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.83PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.49PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.45PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.28PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.04PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 3.74PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.83PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.20PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.04PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.59PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.05PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.56PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.21PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.68PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.27PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.24PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.56PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.44PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.22PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.89PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.20PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.29PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 2.53PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.85PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.21PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.90PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.07PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.67PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.85PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.38PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.40PB/s indexed 373.00B in 0s, 62.58MB/sindexed 1.00TB in 0s, 745.12TB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.23PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.39PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 2.06PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.49PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.07PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.31PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.73PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.49PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.12PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.86PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.24PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.78PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.11PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.31PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.74PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.81PB/s indexed 373.00B in 0s, 52.15MB/s indexed 1.00TB in 0s, 2.04PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.83PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.32PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.30PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.83PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.30PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.39PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.42PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.89PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.16PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.72PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.66PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.47PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.84PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.12PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.99PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.99PB/s indexed 373.00B in 0s, 78.22MB/s indexed 1.00TB in 0s, 1.80PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.65PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.35PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.91PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.68PB/s indexed 373.00B in 0s, 16.13MB/s indexed 1.00TB in 0s, 1.96PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.59PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.44PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.49PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.03PB/s indexed 373.00B in 0s, 47.41MB/s indexed 1.00TB in 0s, 1.18PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.53PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.80PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.18PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.57PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.87PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.60PB/s indexed 373.00B in 0s, 78.22MB/s indexed 1.00TB in 0s, 1.64PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.66PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.81PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.59PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.72PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.36PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.13PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.82PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.60PB/s indexed 373.00B in 0s, 74.50MB/sindexed 1.00TB in 0s, 769.74TB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.31PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.18PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.39PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.58PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.77PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.86PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.25PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.99PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.85PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.32PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.98PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.13PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.75PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.33PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.26PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.43PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.29PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 2.27PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.81PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.01PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.43PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.05PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.16PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.02PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.80PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.31PB/s indexed 373.00B in 0s, 78.22MB/s indexed 1.00TB in 0s, 1.95PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.91PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.53PB/s indexed 373.00B in 0s, 53.95MB/s indexed 1.00TB in 0s, 23.88TB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.86PB/s indexed 373.00B in 0s, 78.22MB/s indexed 1.00TB in 0s, 1.49PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.16PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 2.06PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.81PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.45PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.61PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 2.19PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 2.02PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.79PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.20PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.44PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.22PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.16PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.26PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.44PB/s indexed 373.00B in 0s, 52.15MB/s indexed 1.00TB in 0s, 1.71PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.75PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.68PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 3.00PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.89PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.85PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.36PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.92PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.57PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.72PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.39PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.87PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.60PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.17PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.44PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.56PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.31PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.10PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.65PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.82PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.88PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.28PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.31PB/s indexed 373.00B in 0s, 52.15MB/s indexed 1.00TB in 0s, 2.17PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.98PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.67PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.55PB/s indexed 373.00B in 0s, 74.50MB/sindexed 1.00TB in 0s, 815.06TB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.46PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.41PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.36PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.22PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.39PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.64PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.48PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.63PB/s indexed 373.00B in 0s, 53.95MB/s indexed 1.00TB in 0s, 2.17PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.27PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.74PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.84PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 2.54PB/s indexed 373.00B in 0s, 74.50MB/sindexed 1.00TB in 0s, 290.61TB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.90PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.47PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 2.46PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.08PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.19PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.75PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.56PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.40PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.35PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.30PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.96PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.62PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.09PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.88PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.92PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.02PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.17PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.02PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.20PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.20PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.81PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.37PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.27PB/s indexed 373.00B in 0s, 78.22MB/s indexed 1.00TB in 0s, 2.16PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.77PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.28PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.72PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.80PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.21PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.11PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.36PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 2.30PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.89PB/s indexed 373.00B in 0s, 52.15MB/s indexed 1.00TB in 0s, 2.10PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.95PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.82PB/s indexed 373.00B in 0s, 52.15MB/s indexed 1.00TB in 0s, 1.99PB/s indexed 373.00B in 0s, 62.58MB/sindexed 1.00TB in 0s, 958.70TB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.90PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.84PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.24PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.02PB/s indexed 373.00B in 0s, 52.15MB/s indexed 1.00TB in 0s, 1.20PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.89PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.83PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.69PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.77PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.39PB/s indexed 373.00B in 0s, 78.22MB/s indexed 1.00TB in 0s, 2.83PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.95PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.30PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.75PB/s indexed 373.00B in 0s, 74.50MB/sindexed 1.00TB in 0s, 792.42TB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.80PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.39PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.03PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.05PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.26PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.54PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.49PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.28PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.61PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.58PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.15PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.76PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.46PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.81PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.77PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.86PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.30PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.28PB/s indexed 373.00B in 0s, 53.95MB/s indexed 1.00TB in 0s, 2.04PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.69PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.48PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.26PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.98PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.03PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.15PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.62PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.88PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.65PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.76PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.29PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.17PB/s indexed 373.00B in 0s, 78.22MB/s indexed 1.00TB in 0s, 1.03PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.52PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 4.36PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.88PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.39PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.22PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.91PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.66PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.72PB/s indexed 373.00B in 0s, 74.50MB/sindexed 1.00TB in 0s, 186.43TB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.20PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.10PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.06PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.80PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.23PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.45PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.33PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.48PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.73PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.20PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.80PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.17PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.27PB/s indexed 373.00B in 0s, 74.50MB/sindexed 1.00TB in 0s, 952.39TB/s indexed 373.00B in 0s, 62.58MB/sindexed 1.00TB in 0s, 389.88TB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.29PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.68PB/s indexed 373.00B in 0s, 74.50MB/sindexed 1.00TB in 0s, 992.97TB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.40PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.57PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.49PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 3.26PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.68PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.66PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.18PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.66PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.83PB/s indexed 373.00B in 0s, 41.17MB/s indexed 1.00TB in 0s, 1.18PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.41PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.08PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.31PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.89PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.65PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.40PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.21PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.97PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.93PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.01PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.64PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.73PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.59PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.79PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.85PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.73PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.27PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.81PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.75PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.83PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.82PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.97PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.41PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.32PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.30PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.79PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.90PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.15PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.89PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.79PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.01PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.63PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.51PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.75PB/s indexed 373.00B in 0s, 92.03MB/s indexed 1.00TB in 0s, 1.94PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.11PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.42PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.89PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.94PB/s indexed 373.00B in 0s, 47.41MB/sindexed 1.00TB in 0s, 989.22TB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.73PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.63PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.73PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.38PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.01PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.50PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.71PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.22PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.93PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.07PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.73PB/s indexed 373.00B in 0s, 78.22MB/s indexed 1.00TB in 0s, 1.86PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.28PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.00PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.05PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.71PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.08PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.14PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.40PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.15PB/s indexed 373.00B in 0s, 74.50MB/sindexed 1.00TB in 0s, 304.60TB/s indexed 373.00B in 0s, 74.50MB/sindexed 1.00TB in 0s, 969.11TB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.75PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.98PB/s save(maf_kirc,file = "maf_kirc.rda",compress = "xz")
# KIRP
query_kirp <- GDCquery(
project = c("TCGA-KIRP"),
data.category = "Simple Nucleotide Variation",
access = "open",
data.type = "Masked Somatic Mutation",
workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking"
)## --------------------------------------## o GDCquery: Searching in GDC database## --------------------------------------## Genome of reference: hg38## --------------------------------------------## oo Accessing GDC. This might take a while...## --------------------------------------------## ooo Project: TCGA-KIRP## --------------------## oo Filtering results## --------------------## ooo By access## ooo By data.type## ooo By workflow.type## ----------------## oo Checking data## ----------------## ooo Checking if there are duplicated cases## ooo Checking if there are results for the query## -------------------## o Preparing output## -------------------GDCdownload(query_kirp)## Downloading data for project TCGA-KIRP## Of the 283 files for download 283 already exist.## All samples have been already downloadedmaf_kirp <- GDCprepare(query_kirp)## indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.54PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.92PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.20PB/s indexed 373.00B in 0s, 52.15MB/s indexed 1.00TB in 0s, 2.56PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.13PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.13PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.37PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.38PB/s indexed 373.00B in 0s, 7.02MB/s indexed 1.00TB in 0s, 1.25PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.43PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.11PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.38PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.18PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.47PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.27PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.88PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.25PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.36PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.11PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.75PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.18PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.21PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.72PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.35PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.24PB/s indexed 373.00B in 0s, 62.58MB/sindexed 1.00TB in 0s, 949.58TB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.22PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.18PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.22PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.51PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.31PB/s indexed 373.00B in 0s, 74.50MB/sindexed 1.00TB in 0s, 996.98TB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.16PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.27PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.13PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 2.36PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.74PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.83PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.29PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.67PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.70PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.13PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.59PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.40PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.99PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.17PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.81PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.13PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.62PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.47PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.28PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.80PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.76PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.60PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.50PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.10PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.79PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.63PB/s indexed 373.00B in 0s, 78.22MB/s indexed 1.00TB in 0s, 1.90PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.11PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 3.16PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.08PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.24PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 2.06PB/s indexed 373.00B in 0s, 74.50MB/sindexed 1.00TB in 0s, 920.81TB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.69PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.33PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.18PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.46PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.29PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.09PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.52PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.15PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.77PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.45PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.06PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.71PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.41PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.57PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.98PB/s indexed 373.00B in 0s, 60.17MB/sindexed 1.00TB in 0s, 892.03TB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.34PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.12PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.30PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.46PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.31PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.54PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.49PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.01PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.08PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.17PB/s indexed 373.00B in 0s, 5.84MB/s indexed 1.00TB in 0s, 2.15PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.89PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.35PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 3.13PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.48PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.96PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.59PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.02PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.11PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.16PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.39PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.04PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.36PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.27PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.03PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.25PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.54PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.54PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.51PB/s indexed 373.00B in 0s, 62.58MB/sindexed 1.00TB in 0s, 943.39TB/s indexed 373.00B in 0s, 62.58MB/sindexed 1.00TB in 0s, 535.60TB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.33PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.36PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.23PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.22PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.85PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.02PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.11PB/s indexed 373.00B in 0s, 78.22MB/s indexed 1.00TB in 0s, 2.21PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.69PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.83PB/s indexed 373.00B in 0s, 52.15MB/s indexed 1.00TB in 0s, 37.75TB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.48PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.14PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.29PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.89PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.76PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.42PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.33PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 3.22PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.85PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.75PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.33PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.28PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.13PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.20PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.33PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.00PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.82PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.37PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.14PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.08PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.97PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.55PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.03PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.05PB/s indexed 373.00B in 0s, 78.22MB/s indexed 1.00TB in 0s, 2.32PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.61PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.07PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.30PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.13PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.78PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.93PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.47PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.83PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.15PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.90PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.62PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.22PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.01PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.59PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.18PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.56PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.05PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.17PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.76PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.75PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.85PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.91PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.98PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.09PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.58PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.41PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.94PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.13PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.98PB/s indexed 373.00B in 0s, 78.22MB/s indexed 1.00TB in 0s, 3.17PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.55PB/s indexed 373.00B in 0s, 74.50MB/sindexed 1.00TB in 0s, 823.06TB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.36PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.36PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.52PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.12PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.26PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.65PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.29PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.58PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.62PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.80PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.37PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 3.04PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.47PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.32PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.11PB/s indexed 373.00B in 0s, 60.17MB/sindexed 1.00TB in 0s, 696.38TB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.44PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.00PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 2.95PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.30PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.51PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.44PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.29PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.56PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.99PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.87PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.28PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.99PB/s indexed 373.00B in 0s, 62.58MB/sindexed 1.00TB in 0s, 532.75TB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.73PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.32PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.30PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.76PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.55PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.71PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.98PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.26PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.97PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.18PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.50PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.32PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 2.01PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.33PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.35PB/s indexed 373.00B in 0s, 62.58MB/sindexed 1.00TB in 0s, 814.90TB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.31PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.57PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 2.25PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.84PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.95PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.63PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.28PB/s indexed 373.00B in 0s, 53.95MB/sindexed 1.00TB in 0s, 849.57TB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.21PB/s indexed 373.00B in 0s, 97.78MB/s indexed 1.00TB in 0s, 1.78PB/s indexed 373.00B in 0s, 92.03MB/s indexed 1.00TB in 0s, 1.31PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.23PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.31PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.52PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.70PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.33PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.19PB/s indexed 373.00B in 0s, 46.01MB/s indexed 1.00TB in 0s, 25.65TB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.81PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.27PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.42PB/s indexed 373.00B in 0s, 74.50MB/sindexed 1.00TB in 0s, 716.36TB/s indexed 373.00B in 0s, 74.50MB/sindexed 1.00TB in 0s, 614.19TB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.31PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.92PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.12PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.35PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.22PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.22PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.04PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.02PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.11PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.30PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.82PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.23PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.12PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.36PB/s indexed 373.00B in 0s, 74.50MB/sindexed 1.00TB in 0s, 807.68TB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.03PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.37PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.14PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.14PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 2.16PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 1.14PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.18PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.89PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.79PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.09PB/s indexed 373.00B in 0s, 74.50MB/sindexed 1.00TB in 0s, 688.27TB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.61PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.84PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.92PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.73PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.34PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.38PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.92PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.81PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 1.50PB/s save(maf_kirp,file = "maf_kirp.rda",compress = "xz")
# KICH
query_kich <- GDCquery(
project = c("TCGA-KICH"),
data.category = "Simple Nucleotide Variation",
access = "open",
data.type = "Masked Somatic Mutation",
workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking"
)## --------------------------------------## o GDCquery: Searching in GDC database## --------------------------------------## Genome of reference: hg38## --------------------------------------------## oo Accessing GDC. This might take a while...## --------------------------------------------## ooo Project: TCGA-KICH## --------------------## oo Filtering results## --------------------## ooo By access## ooo By data.type## ooo By workflow.type## ----------------## oo Checking data## ----------------## ooo Checking if there are duplicated cases## ooo Checking if there are results for the query## -------------------## o Preparing output## -------------------GDCdownload(query_kich)## Downloading data for project TCGA-KICH## Of the 66 files for download 66 already exist.## All samples have been already downloadedmaf_kich <- GDCprepare(query_kich)## indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 2.83PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.33PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.12PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.76PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.69PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 3.13PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.92PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.11PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.52PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.84PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.36PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.38PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.21PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.29PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.28PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 3.13PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 3.58PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.55PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.83PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 3.18PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 2.63PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.92PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 3.80PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.88PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.88PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.93PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.38PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.79PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.73PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.37PB/s indexed 373.00B in 0s, 62.58MB/sindexed 1.00TB in 0s, 193.38TB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 3.61PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.95PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.16PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.51PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.88PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 3.46PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 3.82PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 1.31PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 3.16PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.12PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.51PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.83PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 3.31PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.04PB/s indexed 373.00B in 0s, 23.35MB/s indexed 1.00TB in 0s, 2.99PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.75PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 2.40PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 3.45PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 2.56PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 3.76PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 2.46PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 3.50PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.25PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.17PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.08PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.30PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 3.42PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 3.32PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.26PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.33PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.94PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.27PB/s indexed 373.00B in 0s, 74.50MB/s indexed 1.00TB in 0s, 3.34PB/s indexed 373.00B in 0s, 62.58MB/s indexed 1.00TB in 0s, 3.36PB/s indexed 373.00B in 0s, 60.17MB/s indexed 1.00TB in 0s, 2.99PB/s save(maf_kich,file = "maf_kich.rda",compress = "xz")analyze Mutation data
library(maftools)
# maftool tutorial: https://www.bioconductor.org/packages/release/workflows/vignettes/TCGAWorkflow/inst/doc/TCGAWorkflow.html#Genomic_analysis
## add clinical data
# To prepare for maftools we will also include clinical data
# For a mutant vs WT survival analysis
# get indexed clinical patient data for GBM samples
kirc_clin <- GDCquery_clinic(project = "TCGA-KIRC", type = "Clinical")
kirp_clin <- GDCquery_clinic(project = "TCGA-KIRP", type = "Clinical")
kich_clin <- GDCquery_clinic(project = "TCGA-KICH", type = "Clinical")
colnames(kirc_clin)[grep("submitter_id",colnames(kirc_clin))] <- "Tumor_Sample_Barcode"
colnames(kirp_clin)[grep("submitter_id",colnames(kirp_clin))] <- "Tumor_Sample_Barcode"
colnames(kich_clin)[grep("submitter_id",colnames(kich_clin))] <- "Tumor_Sample_Barcode"
# we need to create a binary variable 1 is dead 0 is not dead
plyr::count(kirc_clin$vital_status)kirc_clin$Overall_Survival_Status <- 1 # dead
kirc_clin$Overall_Survival_Status[which(kirc_clin$vital_status != "Dead")] <- 0
# If patient is not dead we don't have days_to_death (NA)
# we will set it as the last day we know the patient is still alive
kirc_clin$time <- kirc_clin$days_to_death
kirc_clin$time[is.na(kirc_clin$days_to_death)] <- kirc_clin$days_to_last_follow_up[is.na(kirc_clin$days_to_death)]
# kirp clinical
# we need to create a binary variable 1 is dead 0 is not dead
plyr::count(kirp_clin$vital_status)kirp_clin$Overall_Survival_Status <- 1 # dead
kirp_clin$Overall_Survival_Status[which(kirp_clin$vital_status != "Dead")] <- 0
# If patient is not dead we don't have days_to_death (NA)
# we will set it as the last day we know the patient is still alive
kirp_clin$time <- kirp_clin$days_to_death
kirp_clin$time[is.na(kirp_clin$days_to_death)] <- kirp_clin$days_to_last_follow_up[is.na(kirp_clin$days_to_death)]
# kich clinical
# we need to create a binary variable 1 is dead 0 is not dead
plyr::count(kich_clin$vital_status)kich_clin$Overall_Survival_Status <- 1 # dead
kich_clin$Overall_Survival_Status[which(kich_clin$vital_status != "Dead")] <- 0
# If patient is not dead we don't have days_to_death (NA)
# we will set it as the last day we know the patient is still alive
kich_clin$time <- kich_clin$days_to_death
kich_clin$time[is.na(kich_clin$days_to_death)] <- kich_clin$days_to_last_follow_up[is.na(kich_clin$days_to_death)]
# Create object to use in maftools
maf_kirc <- read.maf(
maf = maf_kirc,
clinicalData = kirc_clin,
isTCGA = TRUE
)## -Validating
## -Silent variants: 5891
## -Summarizing
## --Mutiple centers found
## BI;BCM;BCM;BI--Possible FLAGS among top ten genes:
## TTN
## MUC16
## -Processing clinical data
## -Finished in 1.646s elapsed (1.552s cpu)maf_kirp <- read.maf(
maf = maf_kirp,
clinicalData = kirp_clin,
isTCGA = TRUE
)## -Validating
## -Silent variants: 4635
## -Summarizing
## --Mutiple centers found
## BCM;BI--Possible FLAGS among top ten genes:
## TTN
## MUC16
## SYNE1
## -Processing clinical data
## -Finished in 1.333s elapsed (1.192s cpu)maf_kich <- read.maf(
maf = maf_kich,
clinicalData = kich_clin,
isTCGA = TRUE
)## -Validating
## -Silent variants: 668
## -Summarizing
## --Possible FLAGS among top ten genes:
## TTN
## MUC16
## -Processing clinical data
## -Finished in 0.159s elapsed (0.157s cpu)plotmafSummary(
maf = maf_kirc,
rmOutlier = TRUE,
addStat = 'median',
dashboard = TRUE
)
plotmafSummary(
maf = maf_kirp,
rmOutlier = TRUE,
addStat = 'median',
dashboard = TRUE
)
plotmafSummary(
maf = maf_kich,
rmOutlier = TRUE,
addStat = 'median',
dashboard = TRUE
)
mafSurvival(
maf = maf_kirc,
genes = "AXL",
time = 'time',
Status = 'Overall_Survival_Status',
isTCGA = TRUE
)## Looking for clinical data in annoatation slot of MAF..## Number of mutated samples for given genes:## AXL
## 2## Median survival..## Group medianTime N
## 1: Mutant 1068 2
## 2: WT 1130 372## Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
## Loglik converged before variable 1 ; coefficient may be infinite.
#mafSurvival(
# maf = maf_kirp,
# genes = "AXL",
# time = 'time',
# Status = 'Overall_Survival_Status',
# isTCGA = TRUE
#)
#mafSurvival(
# maf = maf_kich,
# genes = "AXL",
# time = 'time',
# Status = 'Overall_Survival_Status',
# isTCGA = TRUE
#)
# MET
mafSurvival(
maf = maf_kirc,
genes = "MET",
time = 'time',
Status = 'Overall_Survival_Status',
isTCGA = TRUE
)## Looking for clinical data in annoatation slot of MAF..
## Number of mutated samples for given genes:## MET
## 3## Median survival..## Group medianTime N
## 1: Mutant 127 3
## 2: WT 1130 371
mafSurvival(
maf = maf_kirp,
genes = "MET",
time = 'time',
Status = 'Overall_Survival_Status',
isTCGA = TRUE
)## Looking for clinical data in annoatation slot of MAF..
## Number of mutated samples for given genes:## MET
## 20## Removed 1 samples with NA's## Median survival..## Group medianTime N
## 1: Mutant 884 20
## 2: WT 730 257
#mafSurvival(
# maf = maf_kich,
# genes = "MET",
# time = 'time',
# Status = 'Overall_Survival_Status',
# isTCGA = TRUE
#)
# SRC
mafSurvival(
maf = maf_kirc,
genes = "SRC",
time = 'time',
Status = 'Overall_Survival_Status',
isTCGA = TRUE
)## Looking for clinical data in annoatation slot of MAF..## Number of mutated samples for given genes:## SRC
## 2## Median survival..## Group medianTime N
## 1: Mutant 726 2
## 2: WT 1130 372## Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
## Loglik converged before variable 1 ; coefficient may be infinite.
#mafSurvival(
# maf = maf_kirp,
# genes = "SRC",
# time = 'time',
# Status = 'Overall_Survival_Status',
# isTCGA = TRUE
#)
#mafSurvival(
# maf = maf_kich,
# genes = "SRC",
# time = 'time',
# Status = 'Overall_Survival_Status',
# isTCGA = TRUE
#)let’s check MET mutations in these three cancers
oncoplot(maf = maf_kirc, genes = c('AXL', 'MET', 'SRC'))
oncoplot(maf = maf_kirp, genes = c('AXL', 'MET', 'SRC'))
#oncoplot(maf = maf_kich, genes = c('AXL', 'MET', 'SRC')) # not mutated
png("/Users/tulaykarakulak/Desktop/AXLPaper/Figures/TCGAPlot/kirc_oncoplot.png", width = 8 * 400, height = 8 * 200, res = 300, bg = "transparent")
print(oncoplot(maf = maf_kirc, genes = c('AXL', 'MET', 'SRC')))## [1] "TCGA-B0-5707" "TCGA-CW-6087" "TCGA-EU-5907" "TCGA-B8-4153" "TCGA-CJ-4916"
## [6] "TCGA-A3-3363" "TCGA-BP-5184"dev.off()## quartz_off_screen
## 2png("/Users/tulaykarakulak/Desktop/AXLPaper/Figures/TCGAPlot/kirp_oncoplot.png", width = 8 * 400, height = 8 * 200, res = 300, bg = "transparent")
print(oncoplot(maf = maf_kirp, genes = c('AXL', 'MET', 'SRC')))## [1] "TCGA-4A-A93W" "TCGA-5P-A9KA" "TCGA-A4-7734" "TCGA-A4-7997" "TCGA-AL-3472"
## [6] "TCGA-AL-7173" "TCGA-B1-7332" "TCGA-BQ-5882" "TCGA-BQ-7059" "TCGA-DZ-6132"
## [11] "TCGA-DZ-6135" "TCGA-G7-A8LE" "TCGA-GL-A59R" "TCGA-IA-A40U" "TCGA-IA-A83W"
## [16] "TCGA-IZ-8196" "TCGA-MH-A561" "TCGA-SX-A71S" "TCGA-SX-A7SQ" "TCGA-UZ-A9PJ"dev.off()## quartz_off_screen
## 2png("/Users/tulaykarakulak/Desktop/AXLPaper/Figures/TCGAPlot/kirc_kirp_oncoplot.png", width = 8 * 400, height = 8 * 400, res = 300, bg = "transparent")
print(coOncoplot(m1 = maf_kirc, m2=maf_kirp, m1Name='ccRCC', m2Name='pRCC', genes = c('AXL', 'MET', 'SRC')))## $M1_sample_order
## [1] "TCGA-B0-5707" "TCGA-CW-6087" "TCGA-EU-5907" "TCGA-B8-4153" "TCGA-CJ-4916"
## [6] "TCGA-A3-3363" "TCGA-BP-5184"
##
## $M2_sample_order
## [1] "TCGA-4A-A93W" "TCGA-5P-A9KA" "TCGA-A4-7734" "TCGA-A4-7997" "TCGA-AL-3472"
## [6] "TCGA-AL-7173" "TCGA-B1-7332" "TCGA-BQ-5882" "TCGA-BQ-7059" "TCGA-DZ-6132"
## [11] "TCGA-DZ-6135" "TCGA-G7-A8LE" "TCGA-GL-A59R" "TCGA-IA-A40U" "TCGA-IA-A83W"
## [16] "TCGA-IZ-8196" "TCGA-MH-A561" "TCGA-SX-A71S" "TCGA-SX-A7SQ" "TCGA-UZ-A9PJ"dev.off()## quartz_off_screen
## 2coBarplot(m1 = maf_kirc, m2 = maf_kirp, m1Name = "KIRC", m2Name = "KIRP", genes = c('AXL', 'MET', 'SRC'))